Summer Data Science Fellowship Opportunity

Program: The Data Incubator is an intensive 8 week fellowship that prepares masters students, PhDs, and postdocs in STEM and social science fields seeking industry careers as data scientists. The program is free for Fellows and supported by sponsorships from hundreds of employers across multiple industries. In response to the overwhelming interest in our earlier sessions, we will be holding another fellowship.

Who Should Apply: Anyone who has already obtained a masters or PhD degree or who is within one year of graduating with a masters or PhD is welcome to apply. Applications from international students are welcome. Everyone else is encouraged to sign-up for a future session.

Locations: In addition to the below in-person locations, we will have a remote online session:
• New York City
• San Francisco Bay Area
• Seattle
• Boston
• Washington, DC.

Dates: All sections will be from 2018-06-18 to 2018-08-10.

Application Link: https://www.thedataincubator.com/fellowship.html#apply?ref=wYWRvbGZvZGVAZW1haWwudXNjLmVkdQ==

Data Science in 30 minutes: Learn how to build a data-science project in our upcoming free Data Science in 30-minutes webcast. Signup soon as space is limited.

Learn More: You can learn about our fellows at The New York Times, LinkedIn, Amazon, Capital One, or Palantir. To read about our latest fellow alumni, check out our blog. To learn more about The Data Incubator, check us out on Venture Beat, The Next Web, or Harvard Business Review.

Molecular Biology Seminar Series

Dr. Gavin Sherlock
Stanford University,
Lab Website

“Exploring the Join Distribution of Fitness Effects for Beneficial Mutations in Yeast.”

Friday, March 30, 2018
12:00 PM
RRI 101

Abstract: We previously developed a lineage tracking system to follow the dynamics of adaptive evolution of 500,000 isogenic haploid lineages of Saccharomyces cerevisiae under a glucose limited regime. By tracking the lineage tags over time, we showed that ~20,000 of the lineages gained a beneficial mutation during the experiment, which occurs over only 240 generations. Furthermore, we have also been able to generate a distribution of fitness effects for these lineages (Levy, Blundell et al, Nature (2015)). We isolated thousands of clones belonging to specific lineages, remeasured their fitness, and whole genome sequenced ~120 haploid clones from independent lineages that had gained beneficial mutations. We found that the RAS/cAMP/PKA pathway and the Tor pathway are frequently targets for adaptation under our conditions, uncovering almost 80 mutations in these pathways. In several cases where a gene has a paralog, beneficial mutations are recovered in one paralog significantly more frequently than that other. We have also found that even when mutations affect the same pathway, that the fitness conferred by mutations in a given gene tends to be specific for that gene, and distinct from the fitness effect of mutations in other genes in the pathway (Venkataram et al, Cell (2016)).

We next measured the fitness of these lineages under alternative conditions to determine in what phase of the growth cycle the beneficial mutations provide their fitness benefit, and whether there are within growth cycle fitness tradeoffs. By extending or shortening the length of exponential phase or stationary phase, we found that lineages carrying mutations from the same pathway show similar patterns of fitness change. Furthermore, Ras pathway mutants accrue fitness from spending time in the respiratory growth phase, but this fitness benefit is only manifested in the next growth cycle, as a shortening of lag phase. We also find that these mutants show deleterious effects in stationary phase, suggesting intrinsic tradeoffs between different parts of the growth cycle (Li et al., Current Biology (2018)).

Finally, to generalize beyond closely related experimental conditions, we have evolved both haploid and diploid yeast in several environments, using a double barcode approach, wherein the evolution condition is encoded in the second barcode. We have isolated adaptive clones from each of the conditions, then pooled them, and remeasured their fitness across each of the conditions, to understand how the ways in which beneficial mutants may either be generalists or specialists, and the ways in which they might tradeoff.

Computational Biology Seminar Series

Dr. Todd J. Vision
University of North Carolina at Chapel Hill
Lab Website

“Skeletons, mutants and ontologies: what can we learn from linking phenotypes and genetics on a large scale?”

Thursday March 29, 2018
2:00 PM
RRI 101

Abstract: In contrast to the plethora of computational tools for comparative genomics, there are relatively few for the comparison of phenotype polymorphism and divergence. Yet, the systematics literature is replete with descriptions of phenotype differences among fossil and living organisms. For the past decade, the Phenoscape project has been exploring ways to compute over this kind of descriptive phenotype information by leveraging the ontologies developed within the model organism community. Here, I describe lessons from applying these semantic technologies to test cases in vertebrate skeletal evolution, with a focus on the application of identifying highly diverged, but statistically similar phenotypes. One key question is how well candidate genes obtained using this approach for major events in phenotype evolution, such as the fin-to-limb transition in tetrapods, agree with, conflict with, or complement, candidate genes from literature. Can semantic reasoning over phenotypes augment the expert knowledge of biological specialists?

7th Annual Beyond the PhD and Postdoctoral Career Conference

“R for Bioinformatics” Workshop Series – USC Libraries Bioinformatics

The USC Libraries Bioinformatics Service is pleased to present the “R for Bioinformatics” workshop series. Knowing how to use R is a valuable skillset, as numerous cutting-edge tools for various genomic data analysis are written in R.  This workshop series is aimed at training researchers in the varied applications of R for bioinformatics.

The first two hands-on workshops of this series are designed for those with no or little experiences in R but want to achieve basic competency in R usage. 

Workshop 1—R and Bioinformatics (4 hr)
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for manipulating bioinformatics data

Workshop 2—Bioconductor and EdgeR (4 hr)  
• More commonly used functions for manipulating and visualizing bioinformatics data
• Introduction to bioinformatics package repositories: CRAN and Bioconductor
• Bioinformatics R Packages Case Study 1 - Using EdgeR for Differential Expression analysis.

Before you sign up:
1. Participants are required to attend BOTH workshops.
2. As seating is limited to 10 participants per workshop session, registration is mandatory and must be fulfilled.
3. Participants are required to bring their own laptops.
4. Additional sessions of both workshops may be offered in near future—register to get on the waiting list.

University Park Campus
Workshop 1:      10am to 2pm, Wednesday, March 28th, 2018
Learning Center, Wilson Dental Library (DEN21) 
Workshop 2:      10am to 2pm, Friday, April 6th, 2018
Learning Center, Wilson Dental Library (DEN21)

Health Science Campus
Workshop 1:      10am to 2pm, Tuesday, April 3rd, 2018  
                                East Conference Room (Basement Level), Norris Medical Library
Workshop 2:      10am to 2pm, Tuesday, April 10th, 2018
Computer Classroom (2nd Level), Norris Medical Library

Lunch will be provided at all sessions.  Sign up with the link below: 
https://tinyurl.com/y8cvjj5p

This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.

Please let us know if you have any questions.

Eddie Loh, Yibu Chen, and Meng Li
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics 

Survey on female doctoral students' experiences with pregnancy and parenting

If you are a woman who is pregnant or has become a parent during your doctoral program, please consider taking our anonymous, online survey. We are exploring the supports available to women and the impact of this experience (whether pregnancy, childbirth, pregnancy loss, infertility, or adoption) on women's doctoral studies and career trajectory. This project has been approved by the IRB at Salem State University -- Approval #121517-3.

If you are willing to participate, please click on the link below. If you know someone who might be interested, please pass on the survey link to them. I am happy to answer any questions about this project.

Pursuing a Doctorate & Parenthood: Understanding the Experiences of Female Doctoral Students

Graduate Research Opportunities at DOE National Laboratories

The Department of Energy’s (DOE) Office of Science is pleased to announce that the Office of Science Graduate Student Research (SCGSR) program is now accepting applications for the 2018 Solicitation 1.  Applications are due 5:00pm Eastern Time on Tuesday, May 15, 2018.

Detailed information about the program, including eligibility requirements and access to the online application system, can be found at: https://science.energy.gov/wdts/scgsr/. 

The SCGSR program supports supplemental awards to outstanding U.S. graduate students to conduct part of their graduate thesis research at a DOE national laboratory/facility in collaboration with a DOE laboratory scientist for a period of 3 to 12 consecutive months—with the goal of preparing graduate students for scientific and technical careers critically important to the DOE Office of Science mission.

The SCGSR program is open to current Ph.D. students in qualified graduate programs at accredited U.S. academic institutions, who are conducting their graduate thesis research in targeted areas of importance to the DOE Office of Science. The research opportunity is expected to advance the graduate students’ overall doctoral thesis/dissertation while providing access to the expertise, resources, and capabilities available at the host DOE laboratories/facilities. The supplemental award provides for additional, incremental costs for living and travel expenses directly associated with conducting the SCGSR research project at the DOE host laboratory/facility during the award period.

The Office of Science expects to make approximately 50 awards in 2018 Solicitation 1 cycle, for project periods beginning anytime between October 29, 2018 and March 4, 2019.

Since its inception in 2014, the SCGSR program has provided support to over 300 graduate awardees from more than 100 different universities to conduct thesis research at 17 DOE national laboratories across the nation.

The SCGSR program is sponsored and managed by the DOE Office of Science’s Office of Workforce Development for Teachers and Scientists (WDTS), in collaboration with the six Office of Science research programs offices and the DOE national laboratories/facilities, and program administration support is provided by the Oak Ridge Institute of Science and Education (ORISE).

For any questions, please contact the SCGSR Program Manager, Dr. Ping Ge, at sc.scgsr@science.doe.gov.

Molecular Biology Seminar Series

Dr. Adriana Bankston
Future of Research
Personal website

Making postdocs “less invisible” in academia

Friday, March 23, 2018
12:00 PM
RRI 101

Abstract: Future of Research (FoR) aims to champion, engage and empower early career scientists with evidence-based resources to improve the scientific research endeavor. As part of this goal, we study academic policies that affect postdocs. Postdocs make up a large portion of the biomedical workforce. However, they are typically considered the “invisible” population in academia. Lack of data on postdoc numbers, titles and pay contributes to the difficulty of devising novel, or improving existing, policies for postdocs. Our studies examined national postdoc trends in these areas. We monitored institutional postdoc salary policies as a result of labor law changes; obtained actual postdoc salaries in U.S. public institutions; and found large institutional variability in reporting postdoc numbers in an established NSF survey. Given these findings, we call for better measures to assess postdoc population trends. We hope these efforts will make postdocs a “less invisible” population, and contribute to an overall recognition of the need for increased academic transparency.

Gold, Hovel, and Del Amo Summer Awards

Attached, you will find the announcements (with application forms) for this year's Gold, Hovel and Del Amo summer awards for continuing students. The internal deadline is Friday, March 16. Please submit your applications to Doug Burleson.

   Gold Fellowship Announcement 2018 by uscbiscgrad on Scribd

   Hovel Summer Travel Award 2018 by uscbiscgrad on Scribd

   Del Amo Continuing Announcement 2018 by uscbiscgrad on Scribd

Computational Biology Open Faculty Search Seminar Series

Dr. Xuebing Wu
MIT University
Research Profile

Decoding the noncoding messages in messenger RNAs

Tuesday, March 6
3:30 PM
RRI 101

Abstract: RNA plays central roles in transmitting and regulating genetic information. While the genetic code is simple and universal, the code controlling the spatiotemporal regulation of mRNAs remains poorly understood. My research aims to understand the fundamental mechanisms of gene regulation at the RNA level by using integrated computational and experimental approaches. I will highlight my recent work that has uncovered widespread roles of RNA secondary structures in regulating human mRNA biogenesis and metabolism. In addition, I will discuss my ongoing work on the translation of noncoding sequences in mRNAs and the systematic discovery of mRNAs with protein-independent functions.

7th Annual Beyond the PhD and Postdoctoral Career Conference

Thesis Center Office Hours

Over the next three weeks, the Graduate School will be holding Thesis Center Office Hours. If you will be submitting a thesis/dissertation manuscript this term and need assistance, please schedule an appointment for a one-one-one session.

Office Hours will be held on UPC, in STU 301, and on HSC, in CHP 219, between 3/5 and 3/23.

Make an appointment here

Marine & Environmental Biology Seminar Series

Dr. Holly Moeller
University of California, Santa Barbara
Lab Website

Mixotrophic mediators of planktonic communities: Connecting models with data to predict dynamics and function

Tuesday, March 6
12 PM
AHF 153 (Torrey Webb Room)
 
Abstract: Mixotrophic organisms, which “mix” photosynthesis and heterotrophy to meet their metabolic needs, are widespread in planktonic communities. This physiological trait allows them to function both as primary producers and as grazers, supplementing their carbon needs with photosynthesis when prey are scarce and scavenging materials from other species when nutrient supplies are low. As such, they play an important dual role mediating community production and nutrient cycling. In recent years, mixotrophs have received increasing attention for this reason, with both empirical and theoretical approaches employed to incorporate them into our understanding of marine planktonic communities. In this talk, I describe recent work focused on how mixotroph traits (particularly those governing photophysiology and grazing) determine community dynamics and function. I formulate mechanistic models for the interactions between mixotrophs, their resources, and their competitors, validate these mathematical models with empirical data, and then use the models to interpret field observations of mixotroph abundance. These models identify environmental conditions under which mixotrophs may be the key mediators of ecosystem function, highlighting new avenues for experimentation and incorporation into ocean-scale approaches.